Variant report

Variant	rs1055770
Chromosome Location	chr2:86014780-86014781
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:86007740..86010052-chr2:86013062..86015438,2	K562	blood:
2	chr2:85980611..85983485-chr2:86014274..86016062,2	MCF-7	breast:
3	chr2:86013750..86016057-chr2:86037086..86038756,2	K562	blood:
4	chr2:86013683..86016312-chr2:86025949..86028304,2	MCF-7	breast:
5	chr2:86012601..86015321-chr2:86017209..86019068,2	K562	blood:
6	chr2:86005993..86008298-chr2:86013315..86016426,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GNLY-4	chr2:86014008-86015162	NONHSAT072050

No data

Variant related genes	Relation type
ENSG00000168874	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11679995	1.00[ASN][1000 genomes]
rs11682625	0.86[ASN][1000 genomes]
rs11682709	0.86[ASN][1000 genomes]
rs11691015	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13001375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13035450	1.00[CHB][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13388951	1.00[ASN][1000 genomes]
rs34027204	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34117913	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34284678	0.81[AMR][1000 genomes]
rs35074676	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4832012	1.00[CHB][hapmap]
rs4832013	0.83[CHD][hapmap]
rs4832014	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4832194	1.00[CHB][hapmap]
rs4832198	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs4832199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4832201	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55974755	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71392945	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs736991	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs748064	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs750442	0.95[CEU][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs750443	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7576412	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7609043	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7609084	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7609441	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874469	chr2:85973618-86025251	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv874470	chr2:85973618-86028257	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv874471	chr2:85976645-86021919	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv1001792	chr2:85983107-86016722	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv535805	chr2:85983107-86016722	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1055770	CYP4A22	trans	parietal	SCAN
rs1055770	RNF103	cis	parietal	SCAN
rs1055770	ELMOD3	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86001400-86023000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:86001600-86020000	Weak transcription	Fetal Brain Female	brain
3	chr2:86001600-86023000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:86002200-86015800	Weak transcription	A549	lung
5	chr2:86004800-86017200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:86005400-86019200	Weak transcription	HUVEC	blood vessel
7	chr2:86006600-86019000	Weak transcription	Esophagus	oesophagus
8	chr2:86006800-86020000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:86007000-86015400	Weak transcription	Brain Angular Gyrus	brain
10	chr2:86007000-86019200	Weak transcription	Hela-S3	cervix
11	chr2:86008200-86016000	Weak transcription	Pancreas	Pancrea
12	chr2:86012000-86014800	Genic enhancers	Left Ventricle	heart
13	chr2:86012000-86016400	Enhancers	Right Atrium	heart
14	chr2:86012000-86019000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:86012200-86015200	Genic enhancers	Lung	lung
16	chr2:86012200-86015600	Weak transcription	Brain Substantia Nigra	brain
17	chr2:86012200-86015600	Bivalent Enhancer	Fetal Stomach	stomach
18	chr2:86012400-86015000	Weak transcription	Fetal Brain Male	brain
19	chr2:86012400-86016400	Genic enhancers	Right Ventricle	heart
20	chr2:86012800-86015600	Enhancers	HepG2	liver
21	chr2:86013200-86015400	Genic enhancers	Spleen	Spleen
22	chr2:86013200-86015800	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr2:86013200-86016000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr2:86013200-86017200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:86013200-86017400	Weak transcription	Brain Germinal Matrix	brain
26	chr2:86013200-86023000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:86013400-86017400	Weak transcription	NH-A	brain
28	chr2:86013400-86019000	Weak transcription	Psoas Muscle	Psoas
29	chr2:86013600-86015400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
30	chr2:86013600-86015800	Genic enhancers	Aorta	Aorta
31	chr2:86013600-86017400	Strong transcription	Adipose Nuclei	Adipose
32	chr2:86013600-86017800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:86013600-86019000	Weak transcription	NHDF-Ad	bronchial
34	chr2:86013600-86023200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:86013800-86015000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:86013800-86015400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:86013800-86016800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:86013800-86019200	Weak transcription	HSMMtube	muscle
39	chr2:86014000-86014800	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr2:86014000-86015000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
41	chr2:86014000-86015200	Strong transcription	Colonic Mucosa	Colon
42	chr2:86014000-86015800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:86014000-86015800	Genic enhancers	Stomach Smooth Muscle	stomach
44	chr2:86014000-86015800	Strong transcription	NHLF	lung
45	chr2:86014000-86015800	Strong transcription	Osteobl	bone
46	chr2:86014000-86016000	Strong transcription	Brain Anterior Caudate	brain
47	chr2:86014000-86016000	Strong transcription	Fetal Muscle Leg	muscle
48	chr2:86014000-86016000	Strong transcription	Gastric	stomach
49	chr2:86014000-86016200	Strong transcription	Fetal Intestine Small	intestine
50	chr2:86014000-86017000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links